Two-component systems, composed of a sensor kinase and a response regulator (RR), are a major tool used by microorganisms to adapt to environmental conditions. Typically, phosphorylation of the RR by the sensor kinase results in gene activation. In the case of B. pertussis, the RR BvgA is phosphorylated by the sensor kinase BvgS to yield BvgA-P that binds to the promoter regions of the virulence genes, activating their transcription during infection. These genes include adhesins, needed to adhere to the ciliated epithelial cells within the upper respiratory tract, and toxins, which cause the major symptoms of whooping cough disease. The serologically distinct fimbriae 2 and fimbriae 3, which are composed primarily of the major subunit proteins Fim2 and Fim3, and FhaB, filamentous hemagglutinin subunit, are adhesins that are common components of the acellular pertussis vaccine. To determine the protein-protein and protein-DNA interactions within the activated complexes of BvgAP/RNA polymerase/DNA we have embarked on projects to map the positions of the proteins and DNA using the protein crosslinker BS3 (bissulfosuccinimidylsuberate) and the chemical cleaving reagent FeBABE (iron bromoacetamidobenzyl-EDTA). Our goal is to develop a structural model of the complete activated complex.